relationships between small bodied fishes and...
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RELATIONSHIPS BETWEEN SMALL BODIED FISHES AND CRUSTACEANS AND SUBMERSED AQUATIC VEGETATION: IMPLICATIONS OF HABITAT CHANGE
By
EDWARD VINCENT CAMP
A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE
UNIVERSITY OF FLORIDA
2010
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© 2010 Edward Vincent Camp
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To my parents, Peter and Marcia, whose unwavering support has enabled me to enjoy
pursuing my passions
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ACKNOWLEDGMENTS
I would like to thank all the members of my supervisory committee for their support
and guidance throughout this project. Dr. Bill Pine provided assistance with the study
design, and Dr. Tom Frazer was tremendously influential by mentoring my development
as an ecologist and a professional. Dr. Christie Staudhammer has been hugely helpful
and patient in fostering my understanding of the data analysis components of this
project. I would also like to thank the Florida Fish and Wildlife Conservation
Commission State Wildlife Initiative Grant Program for funding that made this project
possible.
I am also grateful to my fellow students and co-workers. Many people in the FAS
program worked in difficult conditions to help collect and process data for this project,
including Drew Dutterer, Morgan Edwards, Brandon Baker, and Jared Flowers. I am
especially grateful to Jake Tetzlaff who has given me advice and assistance throughout
all aspects of this project. Additionally I would like to acknowledge the impact that Dr.
Dorothy Boorse, Warren Colyer, and Jason Robinson have had on the development of
my scientific understanding and research interests. Finally, I would like to thank my
family and friends and especially Genevieve for understanding and supporting me over
the last several years.
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TABLE OF CONTENTS page
ACKNOWLEDGMENTS .................................................................................................. 4
LIST OF TABLES ............................................................................................................ 6
LIST OF FIGURES .......................................................................................................... 8
ABSTRACT ................................................................................................................... 11
CHAPTER
1 GENERAL INTRODUCTION .................................................................................. 13
Submersed Aquatic Vegetation .............................................................................. 14 Small bodied fish and Macroinvertebrates .............................................................. 15
Research needs and study Objectives ................................................................... 15
2 EXAMINING RELATIONSHIPS BETWEEN SMALL BODIED FISH AND MACROINVERTEBRATES AND SPECIFIC SAV HABITAT TYPE ........................ 17
Introduction ............................................................................................................. 17 Methods .................................................................................................................. 18
Study Location .................................................................................................. 18 Study Species and Sampling Gear ................................................................... 19
Sampling Design and Methods ......................................................................... 19 Analyses ........................................................................................................... 22
Comparisons of overall SFI Density and Diversity among SAV Habitats ... 22
Comparisons of Densities of specific SFI size Classes and Taxa among SAV Habitats .......................................................................................... 23
Comparisons of specific SFI Taxa Densities between Systems................. 23 Results .................................................................................................................... 24
Sampling and Catch Estimation ....................................................................... 24
Comparisons of overall SFI Density and Diversity among Habitats .................. 25 Comparisons of Densities of SFI size Classes and Taxa among Habitats ....... 26
Comparisons of SFI taxa Densities between Systems ..................................... 27 Discussion .............................................................................................................. 27
3 SUMMARY AND CONCLUSIONS .......................................................................... 70
REFERENCES .............................................................................................................. 74
BIOGRAPHICAL SKETCH ............................................................................................ 79
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LIST OF TABLES
Table page 2-1 Specific response variables compared either among SAV habitats, between
rivers, or both. ..................................................................................................... 33
2-2 Proportional species composition of the Chassahowitzka River June 2008 – May 2009 ............................................................................................................ 33
2-3 Proportional species composition of the Homosassa River November 2008 – May 2009 ............................................................................................................ 34
2-4 Repeated measures analysis of variance results for overall SFI density per
m 2 in the Chassahowitzka river, from June 2008-May 2009 ............................... 34
2-5 Repeated measures analysis of variance results for overall SFI diversity in the Chassahowitzka river, from June 2008-May 2009 ........................................ 34
2-6 Repeated measures analysis of variance results for ln-transformed small
sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ............................................................................................................ 34
2-7 Repeated measures analysis of variance results for ln-transformed medium
sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ............................................................................................................ 35
2-8 Repeated measures analysis of variance results for ln-transformed large
sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ............................................................................................................ 35
2-9 Repeated measures analysis of variance results for ln-transformed L. parva
densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ....... 35
2-10 Repeated measures analysis of variance results for ln-transformed
Palaemonetes spp. densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ................................................................................................... 35
2-11 Repeated measures analysis of variance results for ln-transformed Gobiidae
densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ....... 36
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2-12 Repeated measures analysis of variance results for ln-transformed L.
punctatus densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 ............................................................................................................ 36
2-13 Results from comparisons between mean densities per m 2 in the Chassahowitzka and Homosassa rivers using Welch’s two sample T test, p = 0.05 .................................................................................................................... 36
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LIST OF FIGURES
Figure page 2-1 Mapping and sample selection are illustrated. .................................................... 37
2-2 Recovery probabilities for small fish and macroinvertebrates in 5 specific habitat types. ...................................................................................................... 38
2-3 Pearson’s residuals for the ln-transformed overall SFI density repeated measures model for Chassahowitzka River ....................................................... 39
2-4 Pearson’s residuals for overall SFI diversity repeated measures model for Chassahowitzka River ........................................................................................ 40
2-5 Pearson’s residuals for ln-transformed L. parva repeated measures model, Chassahowitzka River ........................................................................................ 41
2-6 Pearson’s residuals for ln-transformed Palaemonetes spp. repeated measures model, Chassahowitzka River ............................................................ 42
2-7 Pearson’s residuals for the ln-transformed L. punctatus repeated measure’s model, Chassahowitzka River ............................................................................ 43
2-8 Pearson’s residuals for the ln-transformed Gobiidae repeated measures model Chassahowitzka River ............................................................................. 44
2-9 Pearson’s residuals of ln-transformed small SFI repeated measures model Chassahowitzka River ........................................................................................ 45
2-10 Pearson’s residuals for ln-transformed medium SFI repeated measure’s model, Chassahowitzka River. ........................................................................... 46
2-11 Pearson’s residuals from large SFI group (not ln transformed) mixed (not repeated measures) model, for the Chassahowitzka River. ............................... 47
2-12 Overall SFI density per m 2 by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. ................................................. 48
2-13 Pairwise comparisons of overall SFI densities per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown. ..................................................... 49
2-14 Mean overall SFI diversity per m 2 and one standard deviation are shown by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. .................................................................................................................. 50
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2-15 Pairwise comparisons of overall SFI diversity per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown. ..................................................... 51
2-16 Mean small SFI density per m 2 and one standard deviation are by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. ........... 52
2-17 Pairwise comparisons of small SFI density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 53
2-18 Mean medium SFI density per m 2 and one standard deviation shown by habitat type and months in the Chassahowitzka River, June 2008 – May 2009. .................................................................................................................. 54
2-19 Pairwise comparisons of medium SFI density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 55
2-20 Mean large SFI density per m 2 and one standard deviation are shown by habitat type and months in the Chassahowitzka River, June 2008 – May 2009. .................................................................................................................. 56
2-21 Pairwise comparisons of large SFI density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 57
2-22 Mean L. parva density per m 2 with one standard deviation are shown by habitat type and month at the Chassahowitzka River, June 2008 – May 2009. . 58
2-23 Pairwise comparisons of L. parva density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. .......................................... 59
2-24 Mean Palaemonetes spp. density per m 2 and one standard deviation are shown by habitat type and months in the Chassahowitzka River, June 2008 – May 2009. ........................................................................................................... 60
2-25 Pairwise comparisons of Palaemonetes spp. density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. .................... 61
2-26 Mean Gobiidae density per m 2 and one standard deviation are shown by habitat type and month in the Chassahowitzka River, June 2008 – May 2009. .. 62
2-27 Pairwise comparisons of Gobiidae density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 63
2-28 Mean L. punctatus density per m 2 with one standard deviation shown by habitat type and month in the Chassahowitzka River, June 2008 – May 2009. .. 64
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2-29 Pairwise comparisons of L. punctatus density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. ................................ 65
2-30 Comparisons of L. parva. mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. ................................................................. 66
2-31 Comparisons of Palaemonetes spp. mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009 .................................................... 67
2-32 Comparisons of Gobiidae mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009 .................................................................. 68
2-33 Comparisons of L. punctatus mean density per m 2 with one standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. ................................................... 69
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Abstract of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science
RELATIONSHIPS BETWEEN SMALL BODIED FISHES AND CRUSTACEANS
AND SUBMERSED AQUATIC VEGETATION: IMPLICATIONS OF HABITAT CHANGE
By
Edward Vincent Camp
May 2010
Chair: William Pine Cochair: Thomas Frazer Major: Fisheries and Aquatic Sciences
Alterations of aquatic habitats can have profound consequences on the
abundances and distributional patterns of associated faunal organisms. Recognition of
this fact has motivated multiple state and federal agency initiatives related to habitat
management, and encouraged a mechanistic understanding of plant-animal
relationships vital for assessing ecological change. I investigated relationships between
specific aquatic habitat types (submerged aquatic vegetation, SAV) and small bodied
fish and macroinvertebrates (SFI) in the Chassahowitzka and Homosassa rivers; spring-
fed rivers along the west coast of peninsular Florida. A decade of research in these
rivers indicates a shift in the SAV communities within each of these systems, with
decreases in rooted macrophytes (e.g., Vallisneria americana and Sagittaria kurziana)
and concomitant increases in the relative abundance of nuisance filamentous
macroalgae. To assess how these shifts in SAV might affect the SFI community I: (1)
determined if SFI assemblages differed between specific types of SAV, (2) analyzed a
suite of response variables to investigate how SFI size groups and species used SAV
habitat types, and (3) made comparisons of SFI abundances between similar systems
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characterized by dissimilar SAV habitat to infer habitat requirements. I sampled SFI
associated with five SAV habitat types. My results suggest that both SFI density and
species composition were significantly related to SAV habitat type. Contrary to common
perception, overall SFI densities were generally highest in filamentous macroalgae.
However, SFI species diversity was lower in filamentous macroalgae in comparison to
rooted macrophytes. Additionally, I found the densities of specific size classes and taxa
of SFI to differ significantly between SAV habitat types, with larger individuals
associated with rooted macrophytes. These findings, in combination with the available
longer-term monitoring data, provide insight into how continued shifts in SAV may affect
the structure and function of Florida’s spring-fed rivers and other aquatic ecosystems.
This information is essential for understanding how habitat-animal relationships impact
the ecology of an ecosystem undergoing broad-scale habitat change, and may be
useful to managers as a decision support tool.
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CHAPTER 1 GENERAL INTRODUCTION
A key goal in the study and management of natural environments is to understand
the ecological consequences of habitat alterations (Rosenfeld and Hatfield 2006). To
understand these consequences it is useful to characterize the relationships between
animals and their habitats, and specifically to assess which habitats are required to
maintain animal populations (Rosenfeld 2003). Required habitats have been defined as
those habitats that are necessary for growth and survival of individuals and the
persistence of species (Rosenfeld 2003), but in practice required habitats have been
often designated as those that animals use or occupy in greater density than other
habitats (Rosenfeld and Boss 2001). While patterns of habitat use are likely to provide
some insight into particular species’ habitat requirements, such patterns alone are
insufficient to reliably indicate required habitat (Van Horne 1983). Designating habitat
requirements from patterns of use alone presumes that animal species could not persist
in habitats other than those they currently use. This presumption has rarely been
validated in aquatic ecosystems (Rosenfeld 2003). Directly assessing animals’
response to a change in habitat is preferable for determining habitat requirements, and
may validate inferences drawn from habitat use (Van Horne 1983; Rosenfeld 2003).
Correspondingly, there is a recognized need for studies combining patterns of habitat
use with such direct assessments, such as controlled manipulative or natural
experiments, to provide stronger insight into how animals’ populations and ecosystem
structure may be impacted by changes in habitat (Hobbs and Hanley 1990; Rosenfeld
and Hatfield 2006).
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Submersed Aquatic Vegetation
Submersed aquatic vegetation (SAV) is a structural habitat found in aquatic
ecosystems that is considered important to many animals (Orth et al. 1984; Heck et al.
1989), and is also perceived to be undergoing widespread changes. A pattern of SAV
change observed globally is the decline in abundance of rooted macrophytes,
particularly of grass-like species (Hauxwell et al. 2003), and concomitant increases in
abundance of filamentous macroalgae (Duarte 1995). These two SAV habitat types
exhibit very dissimilar structural composition and life histories (Hughes et al. 2002).
Rooted macrophytes are relatively slow-growing, long-lived species whose varied
densities and morphological stem and leaf arrangements generally create
heterogeneously structured habitat characterized by larger, differently sized interstitial
spaces (Duffy and Baltz 1998). In contrast, many filamentous macroalgae have a short
life cycle, rapid turnover, and are characterized by dense, fine, similar sized filaments
that provide a more homogenously structured habitat characterized by uniformly small
interstitial spaces (Dodds and Gudder 1994). Rooted macrophytes are also more
resistant to infrequent disturbances, e.g., high flow events, than are filamentous
macroalgae, which may be removed by such disturbances (Duarte 1995). In contrast,
filamentous macroalgae are considered more resilient than rooted macrophytes to
anthropogenic-related frequent or chronic disturbance, e.g., increased nutrient delivery
and decreased water levels. As such disturbances are ongoing, shifts between rooted
macrophytes and filamentous macroalgae are likely to continue. The continuation of
these shifts, combined with differences in the structural composition of these two SAV
habitat types has led to researchers’ and managers’ concern that a shift from rooted
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macrophytes to filamentous macroalgae will have profound and likely adverse
consequences on associated animal communities (Pihl et al. 1995; Wyda et al. 2002).
Small bodied fish and Macroinvertebrates
Shifts in SAV from rooted macrophytes to filamentous macroalgae would likely
affect epibenthic small bodied fish and macroinvertebrates (hereafter SFI) (Deegan et
al. 2002). In most freshwater systems, the SFI community is generally composed of
small (<60 mm) individuals and plays a key role in food web dynamics. While the SFI
community is often abundant in many SAV habitats, it has been found to differ between
species of SAV. For example, Troutman et al. (2007) found that densities of small
bodied fish differed between three SAV types (Hydrilla verticillata, Sagittaria lancifolia,
and Eichhornia crassipes) within the Atchafalaya basin, Louisiana. Similarly, Chick and
McIvor (1997) found SFI use to differ between three SAV types (H. verticillata,
Potamogeton illinoensis, and Panicum hemitomon) in Lake Okeechobee, Florida.
Additionally, SFI communities may differ between differently structured SAV habitats.
Numerous studies have shown SAV structural characteristics, specifically size of
interstitial spaces, to impact SFI foraging success, predation risks, and abundance
(Chick and McIvor 1994; Bartholomew et al. 2000; Warfe and Barmuta 2004). The
relationships between SAV and SFI and the differences between rooted macrophytes
and filamentous macroalgae imply that a shift between these habitats will likely impact
the SFI community, an impact which may alter food web dynamics.
Research needs and study Objectives
Despite the potential ecological implications associated with such widely observed
changes in SAV, few investigations, particularly in freshwater ecosystems, have
examined how the SFI communities may change following the shift from rooted
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macrophytes to filamentous macroalgae (but see Pihl et al. 1995, Deegan et al. 2002).
Such shifts in SAV have been documented over the last several decades in a number of
Florida’s spring fed rivers, including the Chassahowitzka and the Homosassa rivers
(Frazer et al. 2006; Heffernan et al. in press). These river systems historically
supported similar, extensive, rooted macrophyte beds (primarily Vallisneria americana
and Sagittaria kurziana) and fish communities (Odum 1957a, b). Currently, these rivers
are characterized by having very dissimilar SAV habitat (Notestein et al. 2003; Frazer et
al. 2006). Ongoing monitoring efforts in both rivers document that the Chassahowitzka
River currently contains declining rooted macrophytes, and increasing filamentous
macroalgae and unvegetated substrate, whereas the Homosassa River is comprised
almost exclusively of filamentous macroalgae and unvegetated substrate (Frazer et al.
2006). My objective is to understand how this continued shift from rooted macrophytes
to filamentous macroalgae may affect SFI in coastal freshwater rivers by characterizing
which SAV habitats are required by the SFI community. To accomplish this, I combine
inferences drawn from SFI use of specific SAV habitats in the Chassahowitzka River
with inferences drawn from comparisons of habitat specific SFI use between the
Chassahowitzka (intact vegetation) and Homosassa (degraded vegetation) rivers.
Specifically, I ask:
1. Does the overall density and diversity of the SFI community differ between SAV habitat types, specifically between rooted macrophytes (notably V. americana, filamentous macroalgae, and bare substrate?
2. Do the densities of specific size classes and taxa differ between these SAV habitats?
3. Do the densities of key SFI taxa differ among similar habitat types between rivers that differ in respect to SAV?
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CHAPTER 2 EXAMINING RELATIONSHIPS BETWEEN SMALL BODIED FISH AND
MACROINVERTEBRATES AND SPECIFIC SAV HABITAT TYPE
Introduction
Submersed aquatic vegetation (SAV) is a structural habitat found in aquatic
ecosystems that is considered important to many animals (e.g, SFI) (Orth et al. 1984;
Heck et al. 1989), and is also perceived to be undergoing widespread changes. A
pattern of SAV change observed globally is the decline in abundance of rooted
macrophytes, particularly of grass-like species (Hauxwell et al. 2003), and concomitant
increases in abundance of filamentous macroalgae (Duarte 1995). These two SAV
habitat types exhibit very dissimilar structural composition and life histories (Hughes et
al. 2002), and are perceived to be used differently by SFI (Heffernan et al. in press).
Shifts in SAV from rooted macrophytes to filamentous macroalgae would likely
affect SFI (Deegan et al. 2002). The SFI community has been found to differ between
species of SAV (Chick and McIvor 1997; Troutman et al. 2007). Additionally, SFI
communities may differ between differently structured SAV habitats (Chick and McIvor
1994; Bartholomew et al. 2000; Warfe and Barmuta 2004). The relationships between
SAV and SFI and the differences between rooted macrophytes and filamentous
macroalgae imply that a shift between these habitats will likely impact the SFI
community.
Few investigations have examined how SFI communities may change following a
shift from rooted macrophytes to filamentous macroalgae (but see Pihl et al. 1995;
Deegan et al. 2002). Such shifts in SAV have been documented in the Chassahowitzka
and the Homosassa rivers (Frazer et al. 2006; Heffernan et al. in press). The
Chassahowitzka River currently contains declining rooted macrophytes, and increasing
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filamentous macroalgae and bare substrate, whereas the Homosassa River is
comprised almost exclusively of filamentous macroalgae and unvegetated substrate
(Frazer et al. 2006). These shifts are discussed in more detail in Chapter 1.
In Chapter 2, my objective is to understand how this continued shift from rooted
macrophytes to filamentous macroalgae may affect SFI in coastal freshwater rivers by
characterizing which SAV habitats are required by the SFI community. I examine if the
overall density and diversity of the SFI community differs between specific SAV habitat
types, specifically between rooted macrophytes (notably V. americana), filamentous
macroalgae, and bare substrate. I then determine if the densities of specific size
classes and associated taxa differ between these SAV habitats. Finally I assess
whether the densities of key SFI taxa differ among similar habitat types between rivers
that differ in respect to SAV.
Methods
Study Location
The Chassahowitzka and Homosassa rivers are short (8 and 12 km, respectively),
low gradient spring fed rivers on the Gulf coast of peninsular Florida. I conducted my
research in the freshwater portions of both rivers, which are similar with respect to their
physical (temperature, depth, substrate) and chemical (nutrients, salinity)
characteristics, but characterized by markedly different SAV communities (Hoyer et al.
2004; Frazer et al. 2006). Designated as critical habitat areas by the state of Florida,
these spring-fed coastal rivers support freshwater, oligohaline and marine faunal
communities and associated recreational and commercial activities. Natural resource
management agencies and the general public are concerned that the documented shifts
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in SAV habitat may degrade the valuable function of these systems (Hefferenan et al. in
press).
Study Species and Sampling Gear
Small fishes and crustaceans were sampled with a 1 x 1 x 0.75-m throw trap. This
gear type was selected due to its proficiency at capturing small bodied (less than 60
mm) fish and invertebrates in both densely vegetated and unvegetated shallow areas
(Jordan et al. 1997; Rozas and Minello 1997). To sample sites where water depth
exceeded 0.75 m, I created an extension to the trap by attaching a 0.75-m tall, 3-mm
mesh net with floats to the top of the throw trap. I removed SFI from the trap using a
modified 3-mm mesh bar seine with dimensions matching those of the interior of the
throw trap. Because throw traps very rarely captured larger fish occupying higher
trophic levels (Chick and McIvor 1997), all fish captured were included in analyses.
However, my samples commonly captured much smaller macroinvertebrates (e.g.,
amphipods and isopods) that likely occupied lower trophic levels. Such smaller
macroinvertebrates were not collected or included in these analyses. Commonly
captured species collected and analyzed as SFI included rainwater killifish (Lucania
parva), bluefin killifish (Lucania goodei) spotted sunfish (Lepomis punctatus), Gobiidae
species, grass shrimp (Palaemonetes spp.), blue crab (Callinectes sapidus), and
crayfish (Procambarus spp.).
Sampling Design and Methods
I sampled the SFI community monthly in the Chassahowitzka River from June
2008-May 2009, and in the Homosassa River from November 2008-May 2009. During
these months, SFI were sampled in five specific SAV habitat types: (1) V. americana,
(2) Potamogeton spp., (3) filamentous macroalgae (multiple species), (4) mix of
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filamentous macroalgae and V. americana, and (5) unvegetated substrate. To locate
and sample these SAV habitats, I mapped available habitat types within two study
reaches of each river. Within each reach, I selected two transects perpendicular to river
flow and subdivided each transect at 5-m intervals to create sub-transects extending 5-
m upstream and 5-m downstream (parallel to river flow) from the transect (generally 5 to
17 sub-transects per transect, depending on river width). Along each sub-transect,
snorkeling gear was used to map and characterize 1-m 2 ―cells‖ of SAV habitat at 1-m
intervals (Figure 2-1). To assign sampling sites within study reaches each month, I
randomly selected three replicate ―cells‖ per habitat type. If less than three cells were
available to sample in each reach, each month, I searched for the remaining sample
sites in an additional 5-m upstream and downstream from the mapped areas, and
selected the first appropriate sample sites encountered.
To sample each of the selected SAV habitat cells, I deployed the throw trap and
removed and weighed to the nearest 0.1-kg all above ground SAV material from within
the throw trap. Five passes with a bar seine were then made to remove SFI from within
the trap. The SFI captured in each of the five successive bar seine passes were
removed, placed in a bag, and stored on wet ice. If the first three consecutive passes
were completed without recovering a single SFI, the throw trap was considered
depleted (Glancy et al. 2003) and no further passes were made. All SFI samples were
transported to a laboratory in ice slurry and frozen within 24 hours of being collected.
All individuals were subsequently identified to the lowest taxonomic level possible and
measured to the nearest millimeter of total length for fish taxa and carapace length for
crustaceans. Thirty individuals of each taxa from each sample were randomly selected
21
and wet weighed to the nearest 0.0001 gram. Samples were then refrozen for future
analysis.
Because of uncertainty over whether the 5 bar seine passes captured all SFI from
each throw trap sample, I compared counts of total SFI, to estimated abundances of SFI
from each depletion pass using a multinomial depletion approach (Pollock and Gould
1997) as follows:
]})1([ln{
)]}1(ln{[)1(
)]1(ln[{)ln()()1ln(
)]1(ln[)]1([ln)]1(ln[
)|,(
1
1
1
1 1
1 1
x
j
j
j
x
j
j
j
x
j
x
j
jj
x
j
x
j
jj
C
CQ
ppCQCNQC
CNCNN
CpNLL (eq. 1)
where LL = log likelihood ln = natural log N = abundance of SFI p = probability of capture, j = pass number, x = total number of passes, Ci = in pass j, Г(x) = Gamma function which is used to scale factorials of large numbers, Q = 1-Σj=1 to x[p(1-p)j-1].
If estimated catch exceeded the observed catch, confidence intervals around the
catch estimate were calculated. If the upper confidence intervals of the estimate
exceeded observed catch by >5% (indicative of the total catch not representing all SFI,
5%), the estimated catch was used for further analysis. The multinomial depletion
estimates were also used to estimate and compare capture probability between specific
SAV habitats.
22
Analyses
Comparisons of overall SFI Density and Diversity among SAV Habitats
To assess if the SFI community differed between SAV habitat types within a
system, I examined two SFI response metrics--overall density and species diversity.
Overall density was measured as the total number of SFI individuals per m 2 .
Shannon’s index was used to measure species diversity, as follows:
s
i
ii ppH1
))(ln( (2)
where H’=Index of species diversity, s= Number of species pi= Proportion of total sample belonging to ith species
Shannon’s index was chosen over other diversity indices due to its sensitivity to
rare species (Peet 1974; Kwak and Peterson 2007). I analyzed differences in SFI
density and diversity using repeated measures analysis of variance (ANOVA) with the
SAS procedure PROC GLIMMIX (SAS, version 9.2). The ANOVA assumptions of
homoscedastic variance and normally distributed residuals were assessed with plots of
residual versus predicted values. When assumptions were not met, I transformed the
response variable by taking the natural log (ln) of each. For each SFI response metric
ANOVA, fixed effects were SAV habitat type, month, and reach, and all interactions
between these terms. To properly account for autocorrelation between monthly
measures of SFI per SAV habitat type, a random effect was included to group
measurements in each reach by transect combination. If the SAV habitat type effect
was significant (p 0.05) in the repeated measures ANOVA, I used Tukey HSD
(honestly significant differences) tests to determine differences in the mean SFI
23
response metric between pre-planned comparisons of the SAV habitat types V.
americana, filamentous macroalgae, and bare substrate. Vallisneria americana was
chosen to represent the rooted macrophytes due to its availability at study reaches
throughout the study period. I assessed statistical significance using p 0.05, but also
considered statistically insignificant differences for ecological importance.
Comparisons of Densities of specific SFI size Classes and Taxa among SAV Habitats
To determine how SFI size and species might differ between SAV habitat types, I
investigated the density of specific SFI size classes and taxa as seven additional
response variables (Table 2-1). I analyzed densities of small (0-25 mm), medium (26-
50 mm) and large (>50 mm) size classes of SFI, inclusive of all taxa. I also analyzed
the densities of L. parva, Palaemonetes spp., Gobiidae, and L. punctatus, regardless of
size. These species were chosen to represent different guilds of the SFI community—L.
parva was the most ubiquitous, small fish species, Palaemonetes spp. were the most
abundant crustacean species, L. punctatus was the most common larger SFI species,
and Gobiidae species (multiple genera) were used as characteristic of benthic oriented
SFI. Repeated measures ANOVAs and Tukey HSD tests were used as previously
described to determine differences in response between SAV habitat types for each of
these response metrics, except for density of large sized SFI. A paucity of non-zero
data for the density of large SFI prevented the random effect from being included in the
ANOVA.
Comparisons of specific SFI Taxa Densities between Systems
Historically, the Chassahowitzka and Homosassa rivers were thought to support
similar SAV, and likely SFI communities (Odum 1957a, b). However, in recent years,
24
the Homosassa River has undergone significant declines in SAV while the
Chassahowitzka River has maintained a more intact SAV community (Frazer et al.
2006). Differences in the SAV community and in their associated faunal organisms
(Table 2-1) were used to directly assess how SFI are likely to be impacted by
subsequent loss of rooted macrophytes in the Homosassa River. While such a scenario
does not constitute a true manipulative experiment, strong inferences can still be drawn
from comparisons of the SFI community between these dissimilarly vegetated systems
(Rosenfeld 2001). I compared mean densities of L. parva, Palaemonetes spp.,
Gobiidae, and L. punctatus associated with filamentous macroalgae and bare substrate
between the Chassahowitzka and Homosassa rivers over the months November 2008
through May 2009. I also examined differences in system wide densities, by comparing
the mean densities of each species from all available SAV habitat types between each
river. I tested for differences in densities between river systems using a two sample t
test.
Results
Sampling and Catch Estimation
Vallisneria americana, Potamogeton spp., mixed V. americana and filamentous
macroalgae, filamentous macroalgae and unvegetated (bare) substrate were sampled
in the Chassahowitzka River most months (Potamogeton spp. was not present in
November 2008 and April 2009). In the Homosassa River, only filamentous macroalgae
and unvegetated substrate were available for sampling. I collected a total of 314 throw-
trap samples containing 32 species (30,410 individuals) from the aforementioned
habitats within the Chassahowitzka River monthly between June 2008-May 2009. From
monthly sampling of habitats in the Homosassa River, I collected 40 samples
25
comprising 17 species (1,769 individuals) monthly November 2008-May 2009. I report
proportional abundance of the ten most abundant species of each river (Tables 2-2 and
2-3), which comprised 97% and 99% of all organisms observed for the Chassahowitzka
and Homosassa rivers, respectively. For all habitat types, multinomial depletion
estimates of catch were identical to observed catch in nearly every sample, and capture
probability was nearly identical between habitat types (Figures 2-2). Therefore I used
observed catch for all analyses.
Comparisons of overall SFI Density and Diversity among Habitats
Natural log-transformation of overall SFI density resulted in meeting the
assumptions of homoscedasticity (Figures 2-3 – 2-11). The repeated measures
ANOVA for ln-transformed overall SFI density showed the SAV*month interaction was
significant (Table 2-4; p 0.05), indicating differences of SFI densities between SAV
habitats should be investigated on a month to month basis. Similarly, the analysis for
SFI species diversity indicated the SAV*month*reach interaction was significant for SFI
diversity (Table 2-5; p 0.05). However, because the SFI mean diversity differed
between reaches only by magnitude—i.e. patterns between SAV habitat types were
consistent across sites—I focused on differences in SFI diversity between SAV habitats
by month.
Both density and diversity of the SFI community differed between SAV habitats.
Overall density was greater in all vegetated habitats (V. americana and filamentous
macroalgae) than in bare substrate for most months (Figures 2-12 and 2-13). Densities
of SFI in filamentous macroalgae were greater than V. Americana, when differences
occurred between vegetated habitats, (Figures 2-12 and 2-13). Diversity of SFI was
greater in vegetated habitats than bare habitat for all months (Figures 2-14 and 2-15),
26
with SFI diversity higher in V. americana than filamentous macroalgae for most months
when vegetation types differed (Figures 2-14 and 2-15).
Comparisons of Densities of SFI size Classes and Taxa among Habitats
Natural log-transforming each of the specific SFI size classes and taxa response
metrics (Table 2-1) met model assumptions of homoscedasticity in most cases, as
assessed with plots of residuals (Figures 2-5 – 2-11). For each of these transformed
response metrics, the SAV*month interaction term was a significant effect (Tables 2-6 –
2-12). While the SAV*reach*month interaction was significant for Palaemonetes
spp.(Table 2-10), and the SAV*reach interaction was also significant for Gobiidae
(Table 2-11), pairwise examinations revealed differences between reach were in
magnitude only, and patterns in density by SAV habitat were similar between reaches.
Therefore, I focused on differences in the SFI size group and species mean densities
between SAV habitat types on a month to month basis.
Densities of small SFI, medium SFI, large SFI, L. parva, Palaemonetes spp. and L.
punctatus were higher in vegetated habitats than bare substrate for most months
(Figures 3-6,8). Only Gobiidae had consistently similar densities between bare and
vegetated habitats (Figures 2-26 and 2-27). When densities differed between V.
americana and filamentous macroalgae, densities of small SFI and L. parva were
greater in filamentous macroalgae, whereas densities of larger SFI and L. punctatus
were greater in V. americana (Figures 2-16 – 2-17, 2-20 – 2-23, 2-28 – 2-29). Densities
of Palaemonetes spp, Gobiidae, and medium sized SFI rarely differed between
vegetated habitat types (Figures 2-18 – 2-19, 2-24 – 2-27).
27
Comparisons of SFI taxa Densities between Systems
Differences in SFI densities between the Homosassa and Chassahowitzka rivers
varied among key taxa. Densities of both L. parva and Palaemonetes spp. in
filamentous macroalgae, bare substrate, and pooled from all available SAV habitats
were statistically similar between the two rivers (Table 13, Figures 2-30 – 2-31).
However, densities of Palaemonetes spp. were greater in the Chassahowitzka River
across all habitat types. Gobiidae densities in filamentous macroalgae were also similar
between rivers, but Gobiidae densities associated with bare habitats were significantly
greater in the Homosassa River (Table 2-13, Figure 2-32). Cumulative Gobiidae
densities from all habitats available were also greater in the Homosassa River (Table 2-
13). Densities of L. punctatus associated with filamentous macroalgae were
significantly lower in the Homosassa River compared to the Chassahowitzka River,
while densities associated with bare habitat were similar between rivers (Table 2-13,
Figure 2-33).
Discussion
My results suggest strong associations between SFI taxa and SAV habitats in the
Chassahowitzka and Homosassa rivers, and that a shift from rooted macrophytes to
filamentous macroalgae will elicit changes in the SFI community. Larger SFI taxa will
likely decline following the loss of rooted macrophytes, while some smaller SFI species
may flourish in filamentous macroalgae. This use of filamentous macroalgae is
surprising. Dominance of filamentous macroalgae, however, may precipitate a
subsequent shift to bare substrate and elicit additional declines in SFI. Regardless of a
subsequent SAV shift, the decline of larger SFI associated with the loss of rooted
macrophytes may impact higher trophic levels. Overall, inferences of SAV-SFI
28
relationships provided from this study may be useful for identifying broad patterns of
changes occurring in these systems.
My results provide two lines of inference regarding the impacts of a shift from
rooted macrophytes to filamentous macroalgae on SFI communities. Comparisons of
SFI communities among SAV habitats in the Chassahowitzka River provided weak
inference that overall SFI density, and densities of smaller SFI species, like L. parva
and Palaemonetes spp. would not significantly decline following a loss of rooted
macrophytes, while overall diversity and density of larger SFI, like L. punctatus would.
These comparisons suggest that all SFI, with the exception of Gobiidae, would be
negatively affected by a loss of all vegetated habitat (rooted macrophytes and
filamentous macroalgae). Similarly, comparisons of key species densities between the
Chassahowitzka and Homosassa rivers, provided stronger inferences that following the
loss of rooted macrophytes, L. parva, Gobiidae, and Palaemonetes spp. could maintain
their populations (with Palaemonetes spp. perhaps suffering slight declines), but that L.
punctatus populations would decline to very low abundances. The consistency of the
weaker and stronger inferences drawn from my results provides confidence that larger
SFI may require rooted macrophytes, smaller SFI may not, but almost all SFI require
some vegetated habitat.
The SFI communities’ use of filamentous macroalgae contradicted common
perceptions of the ecological values of this habitat type (Deegan et al. 2002, Hughes et
al. 2002), providing new insight and understanding. Concern over increasing
occurrence of filamentous macroalgae in lotic ecosystems is due, in large part, to the
perception that filamentous macroalgae is poor quality habitat for most fish and
29
invertebrates compared to rooted macrophytes (Paerl 1988). My findings of higher SFI
densities in filamentous macroalgae compared to the native rooted macrophyte V.
americana are novel, and may be explained by the relationships between interstitial
space size and size of the SFI in my study. The size of interstitial spaces may affect
SFI predation risk (Warfe and Barmuta 2006) and foraging opportunities (Grenouillet
and Pont 2001), and small fish have been shown to use habitats proportional to their
body size (Bartholomew et al. 2000). Accordingly, the small size of L. parva and
Palaemonetes spp. may allow them to forage and take refuge in the small interstitial
spaces typical of filamentous macroalgae. These smaller sized SFI’s use of filamentous
macroalgae suggests that this habitat is not ―poor‖ habitat for these species’, despite
constituting less complex physical structure.
Shifts in SAV from rooted macrophytes to filamentous macroalgae may precipitate
further complex habitat changes with additional impacts to the SFI community. The life
history characteristics of filamentous macroalgae (self-shading, short life cycle, and low
resilience to stochastic environmental disturbances) predispose this type of SAV to
subsequent temporary or permanent shifts to bare substrate (Dodds and Gudder 1994;
Duarte 1995; Pihl et al. 1994; Valiela et al. 1997). A shift to bare substrate would be
expected to elicit wide-scale declines in abundance of the SFI community, as shown by
this and previous studies comparing SFI abundance and vital rates between vegetated
to unvegetated habitats (Killgore et al. 1989; Pihl et al. 1995; Jordan 2002). Such a
decline in most SFI species could also affect higher trophic levels (Rozas and Odum
1987) and possibly lead to cascading responses within these ecosystems (Carpenter
and Kitchell 1993).
30
The decline in larger SFI concurrent with the observed shift from rooted
macrophytes to filamentous macroalgae is a key result from this study. By providing
recreational fishing opportunities (Dequine 1950), larger SFI such as L. punctatus are
important in and of themselves to these systems. Additionally, these taxa of SFI
provide critical larger sized forage for predators, such as largemouth bass, Micropterus
salmoides (Tetzlaff 2008). Micropterus salmoides and similar predators may require
larger food items to maintain optimal growth rates (Dunlop 2005). Therefore, the
decline of larger SFI associated with a loss of rooted macrophytes may negatively
impact M. salmoides growth rates. This is supported by results from Tetzlaff (2008) that
showed higher adult M. salmoides growth rates in the Chassahowitzka River compared
to the Homosassa River. Taken in concert with my results, these findings suggest a
trophic cascade linkage (Carpenter and Kitchell 1993) between SAV habitat and M.
salmoides growth, and illustrate that the shift from rooted macrophytes to filamentous
macroalgae may have impacts throughout these ecosystems.
The shifts in SFI and SAV observed in this study may be part of a broader pattern
of declining heterogeneously structured aquatic habitat associated with a shift towards
animal communities characterized by lower abundance, less diversity, and/or smaller
dominant species. Such changes have been described as a progression towards biotic
homogeneity (Airoldi et al. 2008). Biotic homogeneity is defined by McKinney and
Lockwood (1999) as ―… a reduction in overall structural complexity, native biota,
functional traits and the expansion of few widespread and less complex broadly tolerant
biota‖. Shifts in aquatic ecosystems to more homogenous habitat types and declines in
species diversity have been documented in a wide variety of ecosystems such as
31
seagrass beds (Hughes et al. 2002), live bottom communities (Thrush and Dayton
2002; Coleman and Williams 2002), and nearshore oyster reefs (Coen et al. 1999,
Eggleston 1999).
The shifts in habitat and associated SFI observed in the Chassahowitzka and
Homosassa rivers may represent a similar example of increasing biotic homogeneity.
Rooted macrophytes feature greater interstitial and patch scale heterogeneity than
filamentous macroalgae, which provides more structural heterogeneity than bare
substrate. Therefore, shifts in habitat from rooted macrophytes to filamentous
macroalgae to bare substrate constitute increasing structural homogeneity. My study
indicates such a shift would likely cause a decline in SFI abundance, species diversity
and abundance of larger species like L. punctatus, and the dominance of a few smaller
species like L. parva or Gobiidae. The findings reported here represent one of the first
reports of a progression to biotic homogeneity in freshwater systems, and may be useful
as a model for describing similar changes in other systems.
Alternative interpretations of my study results and inferences are possible and
should be noted. I relied on observations of the historic similarity and subsequent
changes in SAV habitat in the Chassahowitzka and Homosassa rivers to make
inferences about SFI habitat requirements. However, other factors unrelated to SAV
habitat may have differed between these two rivers, and caused the observed
differences in the SFI community. Additional studies will be useful to validate the
assumptions of this study and strengthen inferences. Manipulative experiments to
assess habitat specific SFI survival and growth would provide a mechanistic
understanding of why certain SFI species change in response to SAV habitat
32
alterations. Additionally, a mechanistic understanding would further strengthen
inferences of how SFI and their predators may be affected by changes in SAV habitat.
Finally, meta-analyses assessing how other changes in habitat structure have affected
associated animals communities in these and other ecosystems may help determine if
patterns of biotic homogeneity are occurring in freshwater lotic ecosystems.
33
Table 2-1. Specific response variables compared either among SAV habitats, between
rivers, or both.
Response Variable Assessed
Density of SFI size classes and taxa among
Chassahowitzka SAV habitats
Comparisons of certain SFI taxa densities within
SAV habitats types between Chassahowitzka
and Homosassa rivers
Density of rainwater killifish (Lucania parva)
Yes
Yes
Density of grass shrimp (Palaemonetes spp.)
Yes Yes
Density of species of the family Gobiidae
Yes Yes
Density of species of spotted sunfish (Lepomis punctatus)
Yes Yes
Density of small sized SFI (individuals < 25-mm)
Yes No
Density of medium sized SFI (individuals 26-50-mm)
Yes No
Density of large sized SFI (individuals >50-mm
Yes No
Table 2-2. Proportional species composition of the Chassahowitzka River June 2008 –
May 2009 Chassahowitzka River
Rank Species Proportion
1 Lucania parva 0.560
2 Palaemonetes spp. 0.196
3 Lepomis punctatus 0.054
4 Lucania goodei 0.047
5 Procambarus spp 0.035
6 Menedia beryllina 0.031
7 Syngnathus scovelli 0.021
8 Grapsidae 0.010
9 Gobiidae 0.008
10 Notropis petersoni 0.008
34
Table 2-3. Proportional species composition of the Homosassa River November 2008 – May 2009
Homosassa River
Rank Species Proportion
1 Lucania parva 0.343
2 Grapsidae family 0.178
3 Gobiidae family 0.152
4 Anchoa mitchilli 0.115
5 Palaemonetes spp 0.101
6 Eucinostomus argenteus 0.051
7 Menedia beryllina 0.032
8 Calinectes sapidus 0.008
9 Gambusia holbrookii 0.006
10 Syngnathus scovelli 0.005
Table 2-4. Repeated measures analysis of variance results for overall ln-transformed
SFI density per m 2 in the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F
Reach 1 10 0.52 0.5207 SAV 4 10 50.73 <.0001
Reach*SAV 4 10 1.17 0.3919 Month 11 34 9.46 <.0001
Reach * Month 11 34 1.36 0.2412 SAV * Month 42 34 1.82 0.0344
SAV * Reach *Month 30 34 0.97 0.4594
Table 2-5. Repeated measures analysis of variance results for overall SFI diversity in
the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F
Reach 1 10 2.95 0.1166 SAV 4 10 27.01 <.0001
Reach*SAV 4 10 0.99 0.4582 Month 11 34 1.13 0.3681
Reach * Month 11 34 2.80 0.0104 SAV * Month 42 34 2.21 0.0096
SAV * Reach *Month 30 34 2.17 0.0152
Table 2-6. Repeated measures analysis of variance results for ln-transformed small
sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009
Effect Num DF Den DF F Value Pr > F
Reach 1 10 2.31 0.1597 SAV 4 10 42.01 <.0001
Reach*SAV 4 10 0.94 0.4796 Month 11 34 7.43 <.0001
Reach * Month 11 34 2.14 0.0440 SAV * Month 42 34 1.75 0.0483
SAV * Reach *Month 30 34 1.25 0.2609
35
Table 2-7. Repeated measures analysis of variance results for ln-transformed medium
sized SFI densities per m 2 in the Chassahowitzka River, from June 2008-May 2009
Effect Num DF Den DF F Value Pr > F
Reach 1 10 0.60 0.4572 SAV 4 10 35.57 <.0001
Reach*SAV 4 10 0.65 0.6378 Month 11 34 15.58 <.0001
Reach * Month 11 34 1.54 0.1611 SAV * Month 42 34 2.08 0.0151
SAV * Reach *Month 30 34 1.13 0.3676
Table 2-8. Repeated measures analysis of variance results for large sized SFI densities
per m 2 in the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F
Reach 1 10 0.00 0.9853 SAV 4 10 0.00 1.000
Reach*SAV 4 10 0.02 0.9988 Month 11 34 0.62 0.8122
Reach * Month 11 34 0.33 0.9791 SAV * Month 42 34 75.55 <.0001
SAV * Reach *Month 30 34 1.07 0.2876
Table 2-9. Repeated measures analysis of variance results for ln-transformed L. parva
densities per m 2 in the Chassahowitzka River, from June 2008-May 2009 Effect Num DF Den DF F Value Pr > F
Reach 1 10 0.20 0.6667 SAV 4 10 52.73 <.0001
Reach*SAV 4 10 1.47 0.2822 Month 11 34 11.42 <.0001
Reach * Month 11 34 3.96 0.0010 SAV * Month 42 34 2.56 0.0029
SAV * Reach *Month 30 34 1.12 0.3709
Table 2-10. Repeated measures analysis of variance results for ln-transformed
Palaemonetes spp. densities per m 2 in the Chassahowitzka River, from June 2008-May 2009
Effect Num DF Den DF F Value Pr > F
Reach 1 10 5.11 0.0474 SAV 4 10 37.04 <.0001
Reach*SAV 4 10 2.81 0.0846 Month 11 34 15.45 <.0001
Reach * Month 11 34 3.45 0.0026 SAV * Month 42 34 3.25 0.0003
SAV * Reach *Month 30 34 1.96 0.0295
36
Table 2-11. Repeated measures analysis of variance results for ln-transformed
Gobiidae densities per m 2 in the Chassahowitzka River, from June 2008-May 2009
Effect Num DF Den DF F Value Pr > F
Reach 1 10 38.25 0.001 SAV 4 10 3.92 0.0363
Reach*SAV 4 10 3.18 0.0628 Month 11 34 7.02 <.0001
Reach * Month 11 34 5.07 0.0001 SAV * Month 42 34 2.61 0.0024
SAV * Reach *Month 30 34 2.88 0.0017
Table 2-12. Repeated measures analysis of variance results for ln-transformed L.
punctatus densities per m 2 in the Chassahowitzka River, from June 2008-May 2009
Effect Num DF Den DF F Value Pr > F
Reach 1 10 3.09 0.1094 SAV 4 10 7.14 0.0055
Reach*SAV 4 10 0.19 0.9368 Month 11 34 2.97 0.0072
Reach * Month 11 34 1.34 0.2435 SAV * Month 42 34 2.38 0.0054
SAV * Reach *Month 30 34 1.26 0.2558
Table 2-13. Results from comparisons between mean densities per m 2 in the Chassahowitzka and Homosassa rivers using Welch’s two sample T test, p = 0.05
Comparison Mean CHA
Mean HOM
t DF p-value
L. parva, macroalgae 46.078 42.500 0.318 21 0.753 L. parva, bare substrate 0.564 3.344 -1.697 33 0.099
L. parva, all habitats 20.288 14.805 1.208 63 0.231 Palaemonetes spp.,
macroalgae 22.89 10.83 1.513 44 0.137
Palaemonetes spp., bare substrate
0 1.690 -1.067 28 0.295
Palaemonetes spp., all habitats
11.298 4.366 1.787 109 0.077
Gobiidae, macroalgae 1.079 8.08 -1.972 11 0.074 Gobiidae, bare substrate 0.256 5.897 -3.199 28 0.003
Gobiidae, all habitats 0.711 6.536 -3.628 40 0.001 L. punctatus, macroalgae 0.474 0.083 2.2793 48 0.027
L. punctatus, bare substrate
0.026 0.000 1 38 0.324
L. punctatus, all habitats 2.209 0.024 5.9972 177 1.097e-08
37
Figure 2-1. Mapping and sample selection are illustrated. The white rectangle shows
sampling universe per transect. The yellow line shows the transect, the short, red lines are sub-transects, shaded polygon represents an example habitat type, such as V. americana. Small squares represent actual throw trap samples.
38
Figure 2-2. Recovery probabilities for small fish and macroinvertebrates in 5 specific
habitat types. Recovery probabilities are given on the x-axis and the probability density function is given on the y-axis.
39
Pearson Residual
-3
-2
-1
0
1
2
3
4
Linear Predictor
-1 0 1 2 3 4 5 6 7
Figure 2-3. Pearson’s residuals for the ln-transformed overall SFI density repeated
measures model for Chassahowitzka River
40
Pearson Residual
-3
-2
-1
0
1
2
3
Linear Predictor
-1 0 1 2
Figure 2-4. Pearson’s residuals for overall SFI diversity repeated measures model for Chassahowitzka River
41
Pearson Residual
-3
-2
-1
0
1
2
3
Linear Predictor
-1 0 1 2 3 4 5 6 7
Figure 2-5. Pearson’s residuals for ln-transformed L. parva repeated measures model, Chassahowitzka River
42
Pearson Residual
-4
-3
-2
-1
0
1
2
3
4
5
Linear Predictor
-1 0 1 2 3
Figure 2-6. Pearson’s residuals for ln-transformed Palaemonetes spp. repeated measures model, Chassahowitzka River
43
Pearson Residual
-3
-2
-1
0
1
2
3
Linear Predictor
-1 0 1 2 3 4
Figure 2-7. Pearson’s residuals for the ln-transformed L. punctatus repeated measure’s model, Chassahowitzka River
44
Pearson Residual
-3
-2
-1
0
1
2
3
4
Linear Predictor
-1 0 1 2 3
Figure 2-8. Pearson’s residuals for the ln-transformed Gobiidae repeated measures
model Chassahowitzka River
45
Pearson Residual
-4
-3
-2
-1
0
1
2
3
4
Linear Predictor
-1 0 1 2 3 4 5 6 7
Figure 2-9. Pearson’s residuals of ln-transformed small SFI repeated measures model
Chassahowitzka River
46
Pearson Residual
-3
-2
-1
0
1
2
3
4
Linear Predictor
-1 0 1 2 3 4 5
Figure 2-10. Pearson’s residuals for ln-transformed medium SFI repeated measure’s
model, Chassahowitzka River.
47
Pearson Residual (Mu scale)
-4
-3
-2
-1
0
1
2
3
4
5
6
7
Mu
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Figure 2-11. Pearson’s residuals from large SFI group (not ln transformed) mixed (not
repeated measures) model, for the Chassahowitzka River.
48
Figure 2-12. Overall SFI density per m 2 by habitat type and months at the Chassahowitzka River, June 2008 – May 2009. Shown with one standard deviation (for clarity). Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
49
Figure 2-13. Pairwise comparisons of overall SFI densities per m 2 between SAV habitat types at the Chassahowitzka
River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
50
Figure 2-14. Mean overall SFI diversity per m 2 and one standard deviation are shown by habitat type and months at the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
51
Figure 2-15. Pairwise comparisons of overall SFI diversity per m 2 between SAV habitat types at the Chassahowitzka
River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
52
Figure 2-16. Mean small SFI density per m 2 and one standard deviation are by habitat type and months at the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
53
Figure 2-17. Pairwise comparisons of small SFI density per m 2 between SAV habitat types at the Chassahowitzka River,
June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
54
Figure 2-18. Mean medium SFI density per m 2 and one standard deviation shown by habitat type and months in the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
55
Figure 2-19. Pairwise comparisons of medium SFI density per m 2 between SAV habitat types at the Chassahowitzka
River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
56
Figure 2-20. Mean large SFI density per m 2 and one standard deviation are shown by habitat type and months in the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
57
Figure 2-21. Pairwise comparisons of large SFI density per m 2 between SAV habitat types at the Chassahowitzka River,
June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
58
Figure 2-22. Mean L. parva density per m 2 with one standard deviation are shown by habitat type and month at the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
59
Figure 2-23. Pairwise comparisons of L. parva density per m 2 between SAV habitat types at the Chassahowitzka River,
June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
60
Figure 2-24. Mean Palaemonetes spp. density per m 2 and one standard deviation are shown by habitat type and months
in the Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
61
Figure 2-25. Pairwise comparisons of Palaemonetes spp. density per m 2 between SAV habitat types at the
Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
62
Figure 2-26. Mean Gobiidae density per m 2 and one standard deviation are shown by habitat type and month in the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
63
Figure 2-27. Pairwise comparisons of Gobiidae density per m 2 between SAV habitat types at the Chassahowitzka River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown.
64
Figure 2-28. Mean L. punctatus density per m 2 with one standard deviation shown by habitat type and month in the
Chassahowitzka River, June 2008 – May 2009. Different letters indicate statistically significant differences (p≤0.05), and asterisks (*) indicate a habitat was not available for sampling.
65
Figure 2-29. Pairwise comparisons of L. punctatus density per m 2 between SAV habitat types at the Chassahowitzka
River, June 2008-May 2009. Mean and 95% confidence intervals around data are shown
66
Figure 2-30. Comparisons of L. parva. mean density per m 2 with one standard
deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa River were lower than or equal to, respectively, that of the Chassahowitzka River.
67
Figure 2-31. Comparisons of Palaemonetes spp. mean density per m 2 with one
standard deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa were lower than or equal to, respectively, that of the Chassahowitzka.
68
Figure 2-32. Comparisons of Gobiidae mean density per m 2 with one standard
deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa were lower than or equal to, respectively, that of the Chassahowitzka.
69
Figure 2-33. Comparisons of L. punctatus mean density per m 2 with one standard
deviation between the Chassahowitzka and Homosassa rivers cumulative over the months November 2008 – May 2009. Asterisks (*) indicate habitat types were not available for sampling. Minus signs (-) and equal signs (=) represent densities in the Homosassa were lower than or equal to, respectively, that of the Chassahowitzka.
70
CHAPTER 3 SUMMARY AND CONCLUSIONS
I found SFI taxa were strongly related to SAV habitats in the Chassahowitzka and
Homosassa rivers, such that a shift from rooted macrophytes to filamentous macroalgae
would likely elicit changes in the SFI community. Larger SFI taxa will likely decline
following the loss of rooted macrophytes, while some smaller SFI species may flourish
in filamentous macroalgae. Dominance of filamentous macroalgale, however, may
precipitate a subsequent shift to bare substrate and elicit additional declines in SFI.
Regardless of a subsequent SAV shift, the decline of larger SFI associated with the loss
of rooted macrophytes may impact higher trophic levels in these ecosystems. Overall,
inferences of SFI/SAV relationships provided from this study may be useful for
identifying broad patterns of changes occurring in these systems.
Both lines of inference (described in detail in Chapter 2) showed consistent
impacts of a shift from rooted macrophytes to filamentous macroalgae on SFI
communities. First, comparisons of SFI communities among SAV habitats in the
Chassahowitzka River provided weak inference that overall SFI density, and densities
of smaller SFI species, like L. parva and Palaemonetes spp. would not significantly
decline following a loss of rooted macrophytes, while overall diversity and density of
larger SFI, like L. punctatus would. Second, comparisons of key species densities
between the Chassahowitzka and Homosassa rivers, provided stronger inferences that
following the loss of rooted macrophytes, L. parva, Gobiidae, and Palaemonetes spp.
could maintain their populations (with Palaemonetes spp. perhaps suffering slight
declines), but that L. punctatus populations would decline to very low abundances. The
consistency of the weaker and stronger inferences drawn from my results provides
71
confidence that larger SFI may require rooted macrophytes, smaller SFI may not, but
almost all SFI require some vegetated habitat.
My findings that SFI communities’ use of filamentous macroalgae in greater
densities than rooted macrophytes are novel and contradicted the common perception
that filamentous macroalgae is of little ecological value (Paerl 1988; Deegan et al. 2002;
Hughes et al. 2002). These unexpected results may be explained by the relationships
between interstitial space size of the SAV habitat types and size of the SFI in my study.
Smaller SFI may use habitat with proportionally smaller interstitial spaces to decrease
predation risk and increase foraging opportunities (Bartholomew et al. 2000; Grenouillet
and Pont 2001; Warfe and Barmuta 2006). Accordingly, the small size of L. parva and
Palaemonetes spp. may allow them to forage and take refuge in the small interstitial
spaces typical of filamentous macroalgae.
The shift in SAV from rooted macrophytes to filamentous macroalgae may
precipitate further complex habitat changes with additional impacts to the SFI
community. The life history characteristics of filamentous macroalgae predispose this
type of SAV to subsequent temporary or permanent shifts to bare substrate (Dodds and
Gudder 1994; Pihl et al. 1994; Duarte 1995; Valiela et al. 1997). A shift to bare
substrate would be expected to elicit wide-scale declines in abundance of the SFI
community, which could also affect higher trophic levels. Such a cascading effect
(Carpenter and Kitchell 1993) is described in greater detail in Chapter 2.
A key result from this study is that the observed shift from rooted macrophytes to
filamentous macroalgae was associated with a decline in larger SFI. Larger SFI such
as L. punctatus are important in and of themselves to these systems (Dequine 1950),
72
and provide critical larger sized forage for predators, such as Micropterus salmoides
(Tetzlaff 2008). Because M. salmoides and similar predators may require larger food
items to maintain optimal growth rates (Dunlop 2005), the decline of larger SFI may
negatively impact M. salmoides growth rates. This is supported by results from Tetzlaff
(2008) that showed higher adult M. salmoides growth rates in the Chassahowitzka River
compared to the Homosassa River. Taken in concert with my results, these findings
suggest a trophic cascade linkage (Carpenter and Kitchell 1993) between SAV habitat
and M. salmoides growth, and illustrate that the shift from rooted macrophytes to
filamentous macroalgae may have impacts throughout these ecosystems.
The shifts in SFI and SAV observed in this study may be part of a broader pattern
of increasing biotic homogeneity. Increasing biotic homogeneity is described as the
decline of the structural complexity of habitat, associated with the decline of more
specialized native taxa and functional groups and the increase of more tolerant fauna
(McKinney and Lockwood 1999). Biotic homogeneity is described in greater detail in
Chapter 2. In these systems, habitat has shifted from rooted macrophyte (more
complex) to filamentous macroalgae (less complex), and may shift further to bare
substrate (least complex). My study indicates these shifts will be associated a decline
in SFI abundance, species diversity and abundance of larger species like L. punctatus,
and the dominance of a few smaller species like L. parva or Gobiidae. These findings
represent one of the first reports of a progression to biotic homogeneity in freshwater
systems, and may be useful as a model for describing similar changes in other systems.
Alternative interpretations of my study results and inferences are possible and
should be noted. I relied on observations of the historic similarity and subsequent
73
changes in SAV habitat in the Chassahowitzka and Homosassa rivers to make
inferences about SFI habitat requirements. However, other factors unrelated to SAV
habitat may have differed between these two rivers, and caused the observed
differences in the SFI community. Additional studies will be useful to validate the
assumptions of this study and strengthen inferences. Manipulative experiments to
assessing habitat specific SFI survival and growth would provide a mechanistic
understanding of why certain SFI species change in response to SAV habitat
alterations. Additionally, a mechanistic understanding would further strengthen
inferences of how SFI and their predators may be affected by changes in SAV habitat.
Finally, meta-analyses assessing how other changes in habitat structure have affected
associated animals communities in these and other ecosystem may help determine the
if patterns of biotic homogeneity are occurring in freshwater lotic ecosystems.
74
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79
BIOGRAPHICAL SKETCH
Edward Camp was born in 1983 in Malden, Massachusetts. He was
homeschooled by his parents throughout grade school and was encouraged to explore
and study the natural world. In 2001, he graduated from Whitinsville Christian High
School and entered Gordon College in Wenham, Massachusetts. At Gordon College
Edward pursued an interdisciplinary academic track by studying communications,
ecology, economics, sociology and political sciences, and studied abroad in New
Zealand, Western Samoa, as well as Washington, USA. In May 2005 Edward
graduated with a degree in environmental studies.
In May 2005, Edward moved to Logan, Utah to begin work as a research assistant
studying Bonneville Cutthroat trout. Over the next several years Edward worked as a
research assistant in Utah, Wyoming, Colorado, New York and Florida and gained
experience studying fish and fisheries. Over these years Edward hiked, ran, skied and
fished some of the most amazing parts of this country.
Upon the completion of his master’s degree, Edward plans to continue his
education by pursuing a Doctor of Philosophy in the study of fisheries. Ultimately,
Edward is interested in coupling an understanding of fish ecology with social and
economic realities to better sustain both the beauty and utility of aquatic ecosystems.